Regarding company change

You risk the current employer preventing you joining the new company by not giving you a No Objection Certificate* (NOC) which is required for the new employer to make an application.

* This is a letter where, because you are breaking a contract, the employer has to confirm they will release you.

You should have entered Malaysia on a VDR (single entry visa) stamped in passport from one of the  Malaysian consulate/HC in India.  If you did not enter this way there will be a few problems apart from the NOC as changing job would not be possible while in Malaysia (you would have to leave and if an application can be made, it would be while you are in India).

There are no permanent jobs for foreigners in Malaysia, because they are always subject to obtaining an employment pass which can be refused at the time of the renewal process - or the employer can decide not to renew the contract of employment. So the term is very misleading.

Just like you are thinking of quitting and moving to another job - the employer can fire you at any time - there is no job security.

There are no immigration benefits in terms of longer-term visas by having a "permanent" job

What does have some significance in terms of immigration is the salary level. For example 3 years working on an EP at a salary of RM15k per month, may lead to a Residence Pass - https://rpt.talentcorp.com.my/

Thanks Gravitas, for the info... but if my agency provide NOC to join new company, will MDec approve the stage-1 process if apply in 1-2 months gap?  Please, let me know. Thanks!

Has the company or the agency given the EP?

Yes, they applied for stage-2 recently...

Then cancel the Stage 2. Its better not to finalise the EP as you don't need a NOC

However, you didn't say who the EP is with (the project company or the agency)

You should have entered on a single entry visa valid for 30 days so hopefully can leave before it expires and the new application can start when you send back your exit visa proof.

I was hired through agency but EP is under private company. Actually, I would like to stay here and do the visa process. If they provide NOC then no need to leave country right?

In theory that is correct but resigning after 1 month I doubt you will get a NOC. You risk being blacklisted if you resign immediately after getting Stage II completed. That is being a shortsighted opportunist.

That's why you should be honest and stop the process to avoid problems in working in Malaysia in the future. You can be completely blocked in working if your proceed.

Thanks Gravitas, better to stay with current company then...